Starting phenix.real_space_refine on Mon Aug 25 06:51:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wdu_37465/08_2025/8wdu_37465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wdu_37465/08_2025/8wdu_37465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wdu_37465/08_2025/8wdu_37465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wdu_37465/08_2025/8wdu_37465.map" model { file = "/net/cci-nas-00/data/ceres_data/8wdu_37465/08_2025/8wdu_37465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wdu_37465/08_2025/8wdu_37465.cif" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 6 9.91 5 Fe 5 7.16 5 P 21 5.49 5 Mg 37 5.21 5 S 96 5.16 5 C 18084 2.51 5 N 3529 2.21 5 O 4496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26274 Number of models: 1 Model: "" Number of chains: 98 Chain: "C" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2429 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 283} Chain: "L" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2210 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "M" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2533 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "H" Number of atoms: 1993 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 1991 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 235} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 259, 1991 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 235} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2041 Chain: "A" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 397 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Chain: "E" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "F" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 397 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 335 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "I" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 324 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "O" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Q" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 331 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "S" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Chain: "T" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "U" Number of atoms: 407 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Conformer: "B" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} bond proxies already assigned to first conformer: 408 Chain: "V" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 335 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "W" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Chain: "X" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "Y" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 470 Classifications: {'peptide': 59} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 54} Chain breaks: 1 Chain: "Z" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "1" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "3" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 498 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "4" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "5" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 355 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "7" Number of atoms: 359 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 39} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 39} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 354 Chain: "8" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "9" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 251 Unusual residues: {' MG': 1, 'HEM': 4, 'PGV': 1, 'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PLM:plan-1': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 552 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 1, 'PGV': 3, 'UQ8': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 88 Planarities with less than four sites: {'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1, 'PGV:plan-3': 3} Unresolved non-hydrogen planarities: 31 Chain: "M" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 515 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 2, 'CRT': 1, 'LMT': 2, 'MQ8': 1, 'PGV': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-4': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'CDL': 1, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 125 Unusual residues: {' CA': 1, 'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "E" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {' CA': 1, 'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'BCL': 1, 'LDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'BCL': 1, 'LDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {' CA': 1, 'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "T" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "5" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "6" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "M" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Y" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "3" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "9" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.32, per 1000 atoms: 0.20 Number of scatterers: 26274 At special positions: 0 Unit cell: (132.714, 121.806, 135.138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 5 26.01 Ca 6 19.99 S 96 16.00 P 21 15.00 Mg 37 11.99 O 4496 8.00 N 3529 7.00 C 18084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=50, symmetry=0 Number of additional bonds: simple=50, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 772.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4774 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 9 sheets defined 67.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.514A pdb=" N VAL C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 102 Processing helix chain 'C' and resid 106 through 110 Processing helix chain 'C' and resid 121 through 141 removed outlier: 3.538A pdb=" N VAL C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.959A pdb=" N CYS C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.813A pdb=" N ASP C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 244 removed outlier: 3.559A pdb=" N ALA C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 252 through 256 removed outlier: 4.177A pdb=" N PHE C 256 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 283 removed outlier: 3.860A pdb=" N THR C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'C' and resid 323 through 331 Proline residue: C 328 - end of helix Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 32 through 57 Processing helix chain 'L' and resid 76 through 80 Processing helix chain 'L' and resid 85 through 88 Processing helix chain 'L' and resid 89 through 118 Processing helix chain 'L' and resid 121 through 139 removed outlier: 3.590A pdb=" N PHE L 129 " --> pdb=" O PHE L 125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA L 130 " --> pdb=" O ALA L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 146 Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 157 through 169 Processing helix chain 'L' and resid 170 through 171 No H-bonds generated for 'chain 'L' and resid 170 through 171' Processing helix chain 'L' and resid 172 through 175 Processing helix chain 'L' and resid 176 through 205 Processing helix chain 'L' and resid 214 through 227 removed outlier: 3.667A pdb=" N PHE L 222 " --> pdb=" O GLU L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 256 Processing helix chain 'L' and resid 264 through 269 removed outlier: 3.711A pdb=" N TRP L 268 " --> pdb=" O GLY L 264 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TRP L 269 " --> pdb=" O TRP L 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 264 through 269' Processing helix chain 'L' and resid 269 through 274 Processing helix chain 'M' and resid 37 through 44 removed outlier: 3.722A pdb=" N ILE M 43 " --> pdb=" O TRP M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 140 Processing helix chain 'M' and resid 144 through 162 Processing helix chain 'M' and resid 162 through 168 Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 179 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 227 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 263 through 287 removed outlier: 3.801A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'M' and resid 315 through 319 removed outlier: 3.664A pdb=" N THR M 319 " --> pdb=" O PRO M 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 35 Processing helix chain 'H' and resid 43 through 49 Processing helix chain 'H' and resid 70 through 73 Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 216 through 222 removed outlier: 3.513A pdb=" N ALA H 220 " --> pdb=" O ALA H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 250 removed outlier: 3.638A pdb=" N GLY H 246 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS H 247 " --> pdb=" O TYR H 243 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU H 248 " --> pdb=" O ALA H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.508A pdb=" N TRP A 9 " --> pdb=" O HIS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.737A pdb=" N LEU D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 38 Processing helix chain 'E' and resid 11 through 44 removed outlier: 3.526A pdb=" N LYS E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 11 removed outlier: 3.761A pdb=" N LEU F 11 " --> pdb=" O ILE F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 39 Processing helix chain 'G' and resid 11 through 44 Processing helix chain 'I' and resid 5 through 11 removed outlier: 4.184A pdb=" N TRP I 9 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN I 10 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 39 Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'K' and resid 13 through 39 Processing helix chain 'N' and resid 11 through 44 removed outlier: 4.004A pdb=" N GLU N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE N 21 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 11 removed outlier: 3.541A pdb=" N TRP O 9 " --> pdb=" O HIS O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 39 Processing helix chain 'P' and resid 11 through 44 Processing helix chain 'Q' and resid 6 through 10 removed outlier: 3.903A pdb=" N TRP Q 9 " --> pdb=" O HIS Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 39 Processing helix chain 'R' and resid 11 through 44 Processing helix chain 'S' and resid 6 through 11 removed outlier: 3.877A pdb=" N TRP S 9 " --> pdb=" O TRP S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 38 Processing helix chain 'T' and resid 11 through 44 Processing helix chain 'U' and resid 4 through 11 removed outlier: 3.544A pdb=" N LYS U 7 " --> pdb=" O ASP U 4 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE U 8 " --> pdb=" O LEU U 5 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP U 9 " --> pdb=" O TRP U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 39 Processing helix chain 'V' and resid 13 through 44 removed outlier: 3.555A pdb=" N HIS V 19 " --> pdb=" O ALA V 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 11 removed outlier: 3.937A pdb=" N LYS W 7 " --> pdb=" O ASP W 4 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP W 9 " --> pdb=" O TRP W 6 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU W 10 " --> pdb=" O LYS W 7 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 38 Processing helix chain 'X' and resid 11 through 44 removed outlier: 3.521A pdb=" N GLY X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE X 21 " --> pdb=" O GLU X 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 11 removed outlier: 3.803A pdb=" N LYS Y 7 " --> pdb=" O ASP Y 4 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP Y 9 " --> pdb=" O TRP Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 38 Processing helix chain 'Z' and resid 11 through 44 removed outlier: 3.564A pdb=" N GLU Z 17 " --> pdb=" O GLU Z 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY Z 20 " --> pdb=" O LYS Z 16 " (cutoff:3.500A) Processing helix chain '1' and resid 7 through 12 Processing helix chain '1' and resid 13 through 39 Processing helix chain '2' and resid 11 through 44 removed outlier: 3.600A pdb=" N GLU 2 17 " --> pdb=" O GLN 2 13 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL 2 23 " --> pdb=" O HIS 2 19 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN 2 24 " --> pdb=" O GLY 2 20 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 12 Processing helix chain '3' and resid 13 through 39 Processing helix chain '3' and resid 43 through 47 Processing helix chain '4' and resid 13 through 44 Processing helix chain '5' and resid 7 through 12 removed outlier: 3.777A pdb=" N ILE 5 11 " --> pdb=" O LYS 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 39 Processing helix chain '5' and resid 40 through 43 removed outlier: 3.630A pdb=" N ASN 5 43 " --> pdb=" O PRO 5 40 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 40 through 43' Processing helix chain '6' and resid 11 through 44 Processing helix chain '7' and resid 5 through 11 Processing helix chain '7' and resid 13 through 39 removed outlier: 3.967A pdb=" N VAL 7 19 " --> pdb=" O ARG 7 15 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 44 Processing helix chain '9' and resid 7 through 12 Processing helix chain '9' and resid 13 through 39 Processing helix chain '0' and resid 11 through 44 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 Processing sheet with id=AA2, first strand: chain 'L' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AA4, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA5, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AA6, first strand: chain 'H' and resid 66 through 68 Processing sheet with id=AA7, first strand: chain 'H' and resid 89 through 91 Processing sheet with id=AA8, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.788A pdb=" N GLU H 183 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL H 170 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR H 181 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL H 172 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE H 179 " --> pdb=" O VAL H 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.518A pdb=" N VAL H 156 " --> pdb=" O ALA H 164 " (cutoff:3.500A) 1328 hydrogen bonds defined for protein. 3748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 9182 1.38 - 1.56: 17396 1.56 - 1.75: 43 1.75 - 1.93: 180 1.93 - 2.11: 156 Bond restraints: 26957 Sorted by residual: bond pdb=" CB7 CDL D 101 " pdb=" OB8 CDL D 101 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL M 407 " pdb=" OA8 CDL M 407 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL M 409 " pdb=" OA8 CDL M 409 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 bond pdb=" CB7 CDL L 311 " pdb=" OB8 CDL L 311 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CA7 CDL L 311 " pdb=" OA8 CDL L 311 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.13e+02 ... (remaining 26952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 35651 5.02 - 10.04: 1293 10.04 - 15.07: 98 15.07 - 20.09: 20 20.09 - 25.11: 12 Bond angle restraints: 37074 Sorted by residual: angle pdb=" N PRO Y 59 " pdb=" CD PRO Y 59 " pdb=" CG PRO Y 59 " ideal model delta sigma weight residual 103.20 84.37 18.83 1.50e+00 4.44e-01 1.58e+02 angle pdb=" CA PRO Y 59 " pdb=" CB PRO Y 59 " pdb=" CG PRO Y 59 " ideal model delta sigma weight residual 104.50 86.85 17.65 1.90e+00 2.77e-01 8.63e+01 angle pdb=" C39 CRT V 102 " pdb=" C38 CRT V 102 " pdb=" O2 CRT V 102 " ideal model delta sigma weight residual 111.76 86.65 25.11 3.00e+00 1.11e-01 7.01e+01 angle pdb=" C40 CRT M 406 " pdb=" C38 CRT M 406 " pdb=" O2 CRT M 406 " ideal model delta sigma weight residual 111.40 86.96 24.44 3.00e+00 1.11e-01 6.64e+01 angle pdb=" C3 CRT J 103 " pdb=" C1 CRT J 103 " pdb=" C4 CRT J 103 " ideal model delta sigma weight residual 108.82 84.72 24.10 3.00e+00 1.11e-01 6.46e+01 ... (remaining 37069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 14291 36.00 - 72.00: 926 72.00 - 108.00: 179 108.00 - 144.00: 59 144.00 - 180.00: 14 Dihedral angle restraints: 15469 sinusoidal: 8098 harmonic: 7371 Sorted by residual: dihedral pdb=" C1 BCL T 101 " pdb=" CGA BCL T 101 " pdb=" O2A BCL T 101 " pdb=" CBA BCL T 101 " ideal model delta sinusoidal sigma weight residual -180.00 -74.32 -105.68 1 6.00e+00 2.78e-02 3.39e+02 dihedral pdb=" C1 BCL F 502 " pdb=" C2 BCL F 502 " pdb=" C3 BCL F 502 " pdb=" C5 BCL F 502 " ideal model delta sinusoidal sigma weight residual -180.00 -0.00 -180.00 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL 3 101 " pdb=" C2 BCL 3 101 " pdb=" C3 BCL 3 101 " pdb=" C5 BCL 3 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.04 -179.96 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 15466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3333 0.080 - 0.160: 354 0.160 - 0.241: 65 0.241 - 0.321: 13 0.321 - 0.401: 7 Chirality restraints: 3772 Sorted by residual: chirality pdb=" CBD BCL M 403 " pdb=" CAD BCL M 403 " pdb=" CGD BCL M 403 " pdb=" CHA BCL M 403 " both_signs ideal model delta sigma weight residual False 2.62 3.02 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CBD BCL R 101 " pdb=" CAD BCL R 101 " pdb=" CGD BCL R 101 " pdb=" CHA BCL R 101 " both_signs ideal model delta sigma weight residual False 2.62 2.26 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CBD BCL V 101 " pdb=" CAD BCL V 101 " pdb=" CGD BCL V 101 " pdb=" CHA BCL V 101 " both_signs ideal model delta sigma weight residual False 2.62 2.26 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 3769 not shown) Planarity restraints: 4374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 0 101 " 0.370 3.00e-02 1.11e+03 3.09e-01 5.30e+02 pdb=" CBA BCL 0 101 " 0.121 3.00e-02 1.11e+03 pdb=" CGA BCL 0 101 " -0.077 3.00e-02 1.11e+03 pdb=" O1A BCL 0 101 " 0.134 3.00e-02 1.11e+03 pdb=" O2A BCL 0 101 " -0.549 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL W 101 " 0.352 3.00e-02 1.11e+03 2.86e-01 4.55e+02 pdb=" CBA BCL W 101 " 0.185 3.00e-02 1.11e+03 pdb=" CGA BCL W 101 " -0.082 3.00e-02 1.11e+03 pdb=" O1A BCL W 101 " 0.038 3.00e-02 1.11e+03 pdb=" O2A BCL W 101 " -0.493 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL K 102 " -0.354 3.00e-02 1.11e+03 2.86e-01 4.54e+02 pdb=" CBA BCL K 102 " -0.194 3.00e-02 1.11e+03 pdb=" CGA BCL K 102 " 0.085 3.00e-02 1.11e+03 pdb=" O1A BCL K 102 " -0.024 3.00e-02 1.11e+03 pdb=" O2A BCL K 102 " 0.488 3.00e-02 1.11e+03 ... (remaining 4371 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 111 2.39 - 3.02: 14469 3.02 - 3.65: 42930 3.65 - 4.27: 71895 4.27 - 4.90: 112864 Nonbonded interactions: 242269 Sorted by model distance: nonbonded pdb=" OE2 GLU M 96 " pdb=" O HOH M 501 " model vdw 1.765 3.040 nonbonded pdb=" OE1 GLU M 96 " pdb=" O HOH M 502 " model vdw 1.806 3.040 nonbonded pdb=" OE1 GLN C 183 " pdb="MG MG C 405 " model vdw 2.031 2.170 nonbonded pdb=" NE2 HIS L 196 " pdb="FE FE M 401 " model vdw 2.071 2.340 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 401 " model vdw 2.073 2.260 ... (remaining 242264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 10 through 47) selection = (chain '2' and resid 10 through 47) selection = (chain '4' and resid 10 through 47) selection = (chain '6' and resid 10 through 47) selection = (chain '8' and resid 10 through 47) selection = (chain 'B' and resid 10 through 47) selection = (chain 'J' and resid 10 through 47) selection = (chain 'N' and resid 10 through 47) selection = (chain 'P' and resid 10 through 47) selection = (chain 'R' and resid 10 through 47) } ncs_group { reference = (chain '1' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain '5' and (resid 5 through 21 or resid 23 through 46)) selection = (chain '7' and (resid 5 through 21 or resid 23 through 46)) selection = (chain '9' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'A' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'I' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'K' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'O' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'Q' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) } ncs_group { reference = (chain 'D' and (resid 2 through 33 or resid 35 through 50 or resid 102 through 1 \ 03)) selection = (chain 'F' and (resid 2 through 33 or resid 35 through 50 or resid 502 through 5 \ 03)) selection = (chain 'S' and (resid 2 through 33 or resid 35 through 50 or resid 102 through 1 \ 03)) selection = (chain 'U' and (resid 2 through 33 or resid 35 through 50 or resid 101 through 1 \ 02)) selection = (chain 'W' and (resid 2 through 33 or resid 35 through 50 or resid 101 through 1 \ 02)) } ncs_group { reference = (chain 'E' and resid 8 through 47) selection = (chain 'G' and resid 8 through 47) selection = (chain 'T' and resid 8 through 47) selection = (chain 'V' and resid 8 through 47) selection = (chain 'X' and resid 8 through 47) selection = (chain 'Z' and resid 8 through 47) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.300 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.465 27007 Z= 1.428 Angle : 1.894 25.111 37074 Z= 0.819 Chirality : 0.057 0.401 3772 Planarity : 0.017 0.309 4374 Dihedral : 24.811 179.998 10695 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.73 % Allowed : 18.61 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.17), residues: 2494 helix: 1.98 (0.13), residues: 1511 sheet: -0.76 (0.77), residues: 41 loop : 0.51 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 15 TYR 0.020 0.002 TYR C 319 PHE 0.026 0.002 PHE V 30 TRP 0.037 0.002 TRP S 6 HIS 0.011 0.002 HIS R 19 Details of bonding type rmsd covalent geometry : bond 0.01859 (26957) covalent geometry : angle 1.89430 (37074) hydrogen bonds : bond 0.18294 ( 1326) hydrogen bonds : angle 6.05960 ( 3748) Misc. bond : bond 0.27226 ( 50) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 0.574 Fit side-chains REVERT: H 75 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7286 (p) REVERT: F 41 GLU cc_start: 0.7606 (tp30) cc_final: 0.7252 (tp30) REVERT: I 8 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5524 (pt) REVERT: P 27 THR cc_start: 0.7498 (m) cc_final: 0.7023 (m) REVERT: X 28 MET cc_start: 0.6580 (tpt) cc_final: 0.6213 (tpt) REVERT: Y 59 PRO cc_start: 0.6371 (Cg_exo) cc_final: 0.5699 (Cg_endo) REVERT: 4 44 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7456 (ttm170) outliers start: 37 outliers final: 26 residues processed: 301 average time/residue: 0.4852 time to fit residues: 173.1513 Evaluate side-chains 284 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain M residue 312 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 4 ASP Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 235 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN C 206 GLN L 219 ASN M 145 HIS H 71 HIS H 192 ASN A 6 HIS B 4 ASN J 24 GLN ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 6 HIS 2 16 GLN ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113040 restraints weight = 34917.253| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.18 r_work: 0.2943 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.319 27007 Z= 0.147 Angle : 0.780 15.879 37074 Z= 0.306 Chirality : 0.042 0.425 3772 Planarity : 0.005 0.068 4374 Dihedral : 20.921 179.991 6184 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.43 % Allowed : 16.14 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.17), residues: 2494 helix: 2.52 (0.12), residues: 1497 sheet: -0.85 (0.78), residues: 41 loop : 0.44 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 15 TYR 0.016 0.002 TYR M 193 PHE 0.020 0.002 PHE L 41 TRP 0.016 0.001 TRP S 6 HIS 0.008 0.001 HIS R 19 Details of bonding type rmsd covalent geometry : bond 0.00339 (26957) covalent geometry : angle 0.77973 (37074) hydrogen bonds : bond 0.05132 ( 1326) hydrogen bonds : angle 4.32749 ( 3748) Misc. bond : bond 0.06681 ( 50) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 0.590 Fit side-chains REVERT: H 48 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6759 (mtp180) REVERT: H 237 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8583 (t70) REVERT: H 259 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5686 (tp) REVERT: A 16 ARG cc_start: 0.8768 (mtt90) cc_final: 0.8533 (mtt90) REVERT: G 12 GLU cc_start: 0.4952 (OUTLIER) cc_final: 0.4298 (mt-10) REVERT: G 21 ILE cc_start: 0.7058 (mp) cc_final: 0.6791 (mt) REVERT: I 8 ILE cc_start: 0.5989 (OUTLIER) cc_final: 0.5742 (pt) REVERT: J 27 THR cc_start: 0.7403 (m) cc_final: 0.7105 (t) REVERT: O 10 GLN cc_start: 0.6337 (OUTLIER) cc_final: 0.6097 (mt0) REVERT: P 27 THR cc_start: 0.8066 (m) cc_final: 0.7698 (m) REVERT: S 10 LEU cc_start: 0.4524 (OUTLIER) cc_final: 0.4306 (mt) REVERT: S 15 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.6217 (ttp-110) REVERT: S 17 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7448 (mp) REVERT: S 41 GLU cc_start: 0.8678 (mp0) cc_final: 0.8475 (mp0) REVERT: 1 7 LYS cc_start: 0.5893 (OUTLIER) cc_final: 0.5600 (mmtp) REVERT: 4 7 MET cc_start: 0.4029 (OUTLIER) cc_final: 0.3681 (mtt) REVERT: 6 30 PHE cc_start: 0.7884 (m-10) cc_final: 0.7667 (m-10) outliers start: 52 outliers final: 14 residues processed: 314 average time/residue: 0.5216 time to fit residues: 195.1530 Evaluate side-chains 283 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain O residue 10 GLN Chi-restraints excluded: chain S residue 10 LEU Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 28 MET Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 7 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 135 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 176 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 150 HIS L 207 GLN L 219 ASN M 74 ASN H 71 HIS H 103 ASN ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.147760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108930 restraints weight = 36000.564| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.27 r_work: 0.2858 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.344 27007 Z= 0.266 Angle : 0.912 17.081 37074 Z= 0.369 Chirality : 0.048 0.409 3772 Planarity : 0.005 0.066 4374 Dihedral : 20.437 179.760 6154 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.31 % Allowed : 15.07 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.16), residues: 2494 helix: 2.06 (0.12), residues: 1504 sheet: -0.87 (0.76), residues: 41 loop : 0.19 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 192 TYR 0.026 0.003 TYR C 319 PHE 0.032 0.003 PHE L 41 TRP 0.017 0.002 TRP 9 9 HIS 0.010 0.002 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00626 (26957) covalent geometry : angle 0.91208 (37074) hydrogen bonds : bond 0.05922 ( 1326) hydrogen bonds : angle 4.51606 ( 3748) Misc. bond : bond 0.07741 ( 50) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 273 time to evaluate : 0.621 Fit side-chains REVERT: L 76 ASP cc_start: 0.8884 (m-30) cc_final: 0.8628 (m-30) REVERT: L 208 LYS cc_start: 0.5886 (OUTLIER) cc_final: 0.5309 (mppt) REVERT: H 75 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7769 (p) REVERT: H 259 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5799 (tp) REVERT: D 41 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7780 (tp30) REVERT: F 41 GLU cc_start: 0.8122 (tp30) cc_final: 0.7889 (tp30) REVERT: G 12 GLU cc_start: 0.4977 (OUTLIER) cc_final: 0.4278 (tt0) REVERT: I 8 ILE cc_start: 0.5889 (OUTLIER) cc_final: 0.5632 (pt) REVERT: J 24 GLN cc_start: 0.6607 (tt0) cc_final: 0.6200 (tp40) REVERT: J 27 THR cc_start: 0.7416 (m) cc_final: 0.7127 (t) REVERT: N 26 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.5999 (mtt) REVERT: P 13 GLN cc_start: 0.4346 (OUTLIER) cc_final: 0.4001 (tm-30) REVERT: P 24 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6347 (mp-120) REVERT: P 27 THR cc_start: 0.8060 (m) cc_final: 0.7668 (m) REVERT: Q 15 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7316 (mtp180) REVERT: S 15 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6216 (ttp-110) REVERT: S 17 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7465 (mp) REVERT: Y 59 PRO cc_start: 0.6734 (Cg_exo) cc_final: 0.6439 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5977 (OUTLIER) cc_final: 0.5723 (mmtp) REVERT: 2 25 SER cc_start: 0.7097 (t) cc_final: 0.6613 (p) REVERT: 2 27 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7364 (m) REVERT: 3 66 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.4818 (ttp-110) REVERT: 4 14 GLU cc_start: 0.4050 (OUTLIER) cc_final: 0.3521 (mm-30) REVERT: 6 30 PHE cc_start: 0.7968 (m-10) cc_final: 0.7762 (m-10) REVERT: 7 13 ASP cc_start: 0.7808 (t0) cc_final: 0.7560 (t0) outliers start: 71 outliers final: 31 residues processed: 316 average time/residue: 0.5166 time to fit residues: 192.7339 Evaluate side-chains 306 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 259 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 7 MET Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 14 GLU Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 6 residue 10 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 161 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN R 13 GLN ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112911 restraints weight = 29935.964| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.01 r_work: 0.2939 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.319 27007 Z= 0.152 Angle : 0.742 16.881 37074 Z= 0.297 Chirality : 0.040 0.407 3772 Planarity : 0.004 0.070 4374 Dihedral : 19.193 179.965 6154 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.89 % Allowed : 15.39 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.16), residues: 2494 helix: 2.37 (0.12), residues: 1499 sheet: -0.91 (0.78), residues: 41 loop : 0.29 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 15 TYR 0.018 0.002 TYR M 193 PHE 0.024 0.002 PHE L 41 TRP 0.015 0.001 TRP 9 9 HIS 0.006 0.001 HIS 0 37 Details of bonding type rmsd covalent geometry : bond 0.00349 (26957) covalent geometry : angle 0.74180 (37074) hydrogen bonds : bond 0.04983 ( 1326) hydrogen bonds : angle 4.24882 ( 3748) Misc. bond : bond 0.06777 ( 50) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 264 time to evaluate : 0.856 Fit side-chains REVERT: L 208 LYS cc_start: 0.5942 (OUTLIER) cc_final: 0.5352 (mppt) REVERT: L 211 GLU cc_start: 0.8048 (pt0) cc_final: 0.7743 (mt-10) REVERT: H 259 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5696 (tp) REVERT: E 28 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7156 (tpp) REVERT: I 8 ILE cc_start: 0.5908 (OUTLIER) cc_final: 0.5615 (pt) REVERT: J 27 THR cc_start: 0.7425 (m) cc_final: 0.7144 (t) REVERT: P 23 VAL cc_start: 0.7250 (OUTLIER) cc_final: 0.6802 (t) REVERT: P 24 GLN cc_start: 0.6735 (OUTLIER) cc_final: 0.6333 (mp-120) REVERT: P 27 THR cc_start: 0.8104 (m) cc_final: 0.7751 (m) REVERT: Q 15 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7274 (mtp180) REVERT: S 15 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.6208 (ttp-110) REVERT: S 17 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7471 (mp) REVERT: Y 38 SER cc_start: 0.8709 (m) cc_final: 0.8490 (p) REVERT: Y 59 PRO cc_start: 0.6760 (Cg_exo) cc_final: 0.6482 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5932 (OUTLIER) cc_final: 0.5686 (mmtp) REVERT: 2 25 SER cc_start: 0.7106 (t) cc_final: 0.6538 (p) REVERT: 2 27 THR cc_start: 0.7752 (OUTLIER) cc_final: 0.7409 (m) REVERT: 7 13 ASP cc_start: 0.7766 (t0) cc_final: 0.7519 (t0) outliers start: 62 outliers final: 29 residues processed: 309 average time/residue: 0.5085 time to fit residues: 186.3311 Evaluate side-chains 294 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 28 MET Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 244 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 8 optimal weight: 0.0040 chunk 47 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110771 restraints weight = 35721.855| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.23 r_work: 0.2904 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.321 27007 Z= 0.165 Angle : 0.759 16.908 37074 Z= 0.304 Chirality : 0.041 0.402 3772 Planarity : 0.005 0.068 4374 Dihedral : 18.853 179.868 6154 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.03 % Allowed : 15.39 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.16), residues: 2494 helix: 2.37 (0.12), residues: 1502 sheet: -0.98 (0.78), residues: 41 loop : 0.27 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 15 TYR 0.020 0.002 TYR C 319 PHE 0.024 0.002 PHE L 41 TRP 0.014 0.001 TRP 9 9 HIS 0.007 0.002 HIS 0 37 Details of bonding type rmsd covalent geometry : bond 0.00382 (26957) covalent geometry : angle 0.75855 (37074) hydrogen bonds : bond 0.05059 ( 1326) hydrogen bonds : angle 4.25089 ( 3748) Misc. bond : bond 0.06692 ( 50) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 268 time to evaluate : 0.872 Fit side-chains REVERT: L 208 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5342 (mppt) REVERT: H 48 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6767 (mtp180) REVERT: H 253 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6973 (mm-30) REVERT: H 259 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5750 (tp) REVERT: D 6 TRP cc_start: 0.5520 (p-90) cc_final: 0.5266 (p-90) REVERT: E 28 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7168 (tpp) REVERT: F 16 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6296 (mtt90) REVERT: I 8 ILE cc_start: 0.5910 (OUTLIER) cc_final: 0.5626 (pt) REVERT: J 24 GLN cc_start: 0.6605 (tt0) cc_final: 0.6213 (tp40) REVERT: J 27 THR cc_start: 0.7426 (m) cc_final: 0.7123 (t) REVERT: P 23 VAL cc_start: 0.7215 (OUTLIER) cc_final: 0.6752 (t) REVERT: P 24 GLN cc_start: 0.6721 (OUTLIER) cc_final: 0.6346 (mp-120) REVERT: P 27 THR cc_start: 0.8112 (m) cc_final: 0.7760 (m) REVERT: Q 15 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7286 (mtp180) REVERT: S 15 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.6211 (ttp-110) REVERT: S 17 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7465 (mp) REVERT: Y 38 SER cc_start: 0.8764 (m) cc_final: 0.8537 (p) REVERT: Y 59 PRO cc_start: 0.6714 (Cg_exo) cc_final: 0.6426 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5979 (OUTLIER) cc_final: 0.5742 (mmtp) REVERT: 2 7 MET cc_start: 0.3572 (mmp) cc_final: 0.2686 (tpt) REVERT: 2 25 SER cc_start: 0.7177 (OUTLIER) cc_final: 0.6665 (p) REVERT: 2 27 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.7387 (m) REVERT: 7 13 ASP cc_start: 0.7729 (t0) cc_final: 0.7447 (t0) REVERT: 8 26 MET cc_start: 0.8385 (ttm) cc_final: 0.8067 (ttm) outliers start: 65 outliers final: 35 residues processed: 316 average time/residue: 0.5181 time to fit residues: 194.6568 Evaluate side-chains 307 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 28 MET Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 212 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 4 optimal weight: 0.0370 chunk 190 optimal weight: 0.9980 chunk 3 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116016 restraints weight = 29970.349| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.00 r_work: 0.2990 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.263 27007 Z= 0.121 Angle : 0.675 16.529 37074 Z= 0.268 Chirality : 0.038 0.396 3772 Planarity : 0.004 0.068 4374 Dihedral : 17.830 179.971 6154 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.15 % Allowed : 16.70 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.16), residues: 2494 helix: 2.86 (0.12), residues: 1461 sheet: -0.87 (0.81), residues: 41 loop : 0.38 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 9 15 TYR 0.016 0.001 TYR M 193 PHE 0.018 0.001 PHE L 41 TRP 0.021 0.001 TRP S 6 HIS 0.006 0.001 HIS R 19 Details of bonding type rmsd covalent geometry : bond 0.00277 (26957) covalent geometry : angle 0.67470 (37074) hydrogen bonds : bond 0.04461 ( 1326) hydrogen bonds : angle 4.06086 ( 3748) Misc. bond : bond 0.05300 ( 50) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 0.904 Fit side-chains REVERT: L 208 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.5352 (mppt) REVERT: L 211 GLU cc_start: 0.7971 (pt0) cc_final: 0.7655 (mt-10) REVERT: H 48 ARG cc_start: 0.7063 (mtp180) cc_final: 0.6705 (mtp85) REVERT: H 253 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6856 (mm-30) REVERT: H 259 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5724 (tp) REVERT: E 47 LEU cc_start: 0.7828 (mt) cc_final: 0.7623 (mt) REVERT: F 15 ARG cc_start: 0.6184 (tmt90) cc_final: 0.5651 (tmm160) REVERT: J 27 THR cc_start: 0.7387 (m) cc_final: 0.7080 (t) REVERT: P 23 VAL cc_start: 0.7198 (OUTLIER) cc_final: 0.6769 (t) REVERT: P 24 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.6297 (mp-120) REVERT: P 27 THR cc_start: 0.8091 (m) cc_final: 0.7770 (m) REVERT: S 17 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7417 (mp) REVERT: Y 38 SER cc_start: 0.8666 (m) cc_final: 0.8455 (p) REVERT: Y 41 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: Z 7 MET cc_start: 0.2159 (mmt) cc_final: 0.1715 (mtp) REVERT: 1 7 LYS cc_start: 0.5867 (OUTLIER) cc_final: 0.5637 (mmtp) REVERT: 2 7 MET cc_start: 0.3389 (mmp) cc_final: 0.2608 (tpt) REVERT: 2 25 SER cc_start: 0.6980 (t) cc_final: 0.6373 (p) REVERT: 2 27 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7359 (m) REVERT: 3 16 MET cc_start: 0.5733 (mmt) cc_final: 0.5359 (tpt) REVERT: 4 7 MET cc_start: 0.4442 (mtm) cc_final: 0.4154 (ptm) REVERT: 5 22 PHE cc_start: 0.7714 (m-80) cc_final: 0.7399 (m-80) REVERT: 6 30 PHE cc_start: 0.7866 (m-10) cc_final: 0.7658 (m-10) REVERT: 8 26 MET cc_start: 0.8309 (ttm) cc_final: 0.7934 (ttm) outliers start: 46 outliers final: 24 residues processed: 312 average time/residue: 0.5222 time to fit residues: 193.2356 Evaluate side-chains 294 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 32 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 10 GLN 0 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.147303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107778 restraints weight = 33549.424| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.38 r_work: 0.2842 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.339 27007 Z= 0.273 Angle : 0.915 16.657 37074 Z= 0.369 Chirality : 0.048 0.409 3772 Planarity : 0.005 0.063 4374 Dihedral : 19.531 179.929 6147 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.85 % Allowed : 16.18 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.16), residues: 2494 helix: 2.11 (0.12), residues: 1508 sheet: -0.95 (0.77), residues: 41 loop : 0.21 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 192 TYR 0.029 0.003 TYR C 319 PHE 0.033 0.003 PHE L 41 TRP 0.017 0.002 TRP 9 9 HIS 0.011 0.003 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00640 (26957) covalent geometry : angle 0.91471 (37074) hydrogen bonds : bond 0.05767 ( 1326) hydrogen bonds : angle 4.44988 ( 3748) Misc. bond : bond 0.07581 ( 50) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 0.666 Fit side-chains REVERT: L 76 ASP cc_start: 0.8892 (m-30) cc_final: 0.8649 (m-30) REVERT: L 208 LYS cc_start: 0.5872 (OUTLIER) cc_final: 0.5272 (mppt) REVERT: H 253 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6973 (mm-30) REVERT: H 259 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5766 (tp) REVERT: D 6 TRP cc_start: 0.5521 (p-90) cc_final: 0.5278 (p-90) REVERT: F 16 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6312 (mtt90) REVERT: F 41 GLU cc_start: 0.8074 (tp30) cc_final: 0.7827 (tp30) REVERT: J 24 GLN cc_start: 0.6601 (tt0) cc_final: 0.6216 (tp40) REVERT: J 27 THR cc_start: 0.7437 (m) cc_final: 0.7129 (t) REVERT: P 24 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6373 (mp-120) REVERT: P 27 THR cc_start: 0.8048 (m) cc_final: 0.7679 (m) REVERT: Q 15 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7290 (mtp180) REVERT: S 15 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.5794 (ttp-170) REVERT: S 17 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7465 (mp) REVERT: Y 59 PRO cc_start: 0.6664 (Cg_exo) cc_final: 0.6395 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5726 (mmtp) REVERT: 1 18 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6635 (mp) REVERT: 2 7 MET cc_start: 0.3396 (mmp) cc_final: 0.2582 (tpt) REVERT: 2 25 SER cc_start: 0.7276 (OUTLIER) cc_final: 0.6868 (p) REVERT: 3 66 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.4722 (ttp-110) REVERT: 4 7 MET cc_start: 0.4708 (mtm) cc_final: 0.4359 (ptm) REVERT: 6 30 PHE cc_start: 0.8008 (m-10) cc_final: 0.7786 (m-10) REVERT: 7 13 ASP cc_start: 0.7823 (t0) cc_final: 0.7561 (t0) REVERT: 8 26 MET cc_start: 0.8411 (ttm) cc_final: 0.8150 (ttm) outliers start: 61 outliers final: 30 residues processed: 306 average time/residue: 0.5218 time to fit residues: 189.5080 Evaluate side-chains 293 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 6 residue 10 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 194 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.109739 restraints weight = 32277.175| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.37 r_work: 0.2858 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.329 27007 Z= 0.180 Angle : 0.787 16.671 37074 Z= 0.316 Chirality : 0.042 0.406 3772 Planarity : 0.005 0.070 4374 Dihedral : 18.855 179.964 6147 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.19 % Allowed : 16.70 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.16), residues: 2494 helix: 2.26 (0.12), residues: 1498 sheet: -0.99 (0.77), residues: 41 loop : 0.20 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 15 TYR 0.022 0.002 TYR C 319 PHE 0.027 0.002 PHE L 41 TRP 0.022 0.002 TRP S 6 HIS 0.009 0.002 HIS R 19 Details of bonding type rmsd covalent geometry : bond 0.00419 (26957) covalent geometry : angle 0.78672 (37074) hydrogen bonds : bond 0.05187 ( 1326) hydrogen bonds : angle 4.30359 ( 3748) Misc. bond : bond 0.07112 ( 50) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 264 time to evaluate : 0.645 Fit side-chains REVERT: L 208 LYS cc_start: 0.5917 (OUTLIER) cc_final: 0.5308 (mppt) REVERT: L 211 GLU cc_start: 0.8054 (pt0) cc_final: 0.7738 (mt-10) REVERT: H 48 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6831 (mtp180) REVERT: H 253 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6953 (mm-30) REVERT: H 259 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5748 (tp) REVERT: D 41 GLU cc_start: 0.8311 (tp30) cc_final: 0.7866 (tp30) REVERT: J 24 GLN cc_start: 0.6606 (tt0) cc_final: 0.6223 (tp40) REVERT: J 27 THR cc_start: 0.7434 (m) cc_final: 0.7119 (t) REVERT: P 23 VAL cc_start: 0.7216 (OUTLIER) cc_final: 0.6748 (t) REVERT: P 24 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6350 (mp-120) REVERT: P 27 THR cc_start: 0.8080 (m) cc_final: 0.7733 (m) REVERT: S 15 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.5773 (ttp-170) REVERT: S 17 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7485 (mp) REVERT: Y 59 PRO cc_start: 0.6671 (Cg_exo) cc_final: 0.6407 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5699 (mmtp) REVERT: 1 18 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6636 (mp) REVERT: 2 7 MET cc_start: 0.3397 (mmp) cc_final: 0.2595 (tpt) REVERT: 2 25 SER cc_start: 0.7241 (OUTLIER) cc_final: 0.6807 (p) REVERT: 2 27 THR cc_start: 0.7654 (t) cc_final: 0.7312 (m) REVERT: 4 7 MET cc_start: 0.4662 (mtm) cc_final: 0.4329 (ptm) REVERT: 6 30 PHE cc_start: 0.8034 (m-10) cc_final: 0.7794 (m-10) REVERT: 7 13 ASP cc_start: 0.7793 (t0) cc_final: 0.7552 (t0) REVERT: 8 26 MET cc_start: 0.8416 (ttm) cc_final: 0.8160 (ttm) outliers start: 47 outliers final: 29 residues processed: 298 average time/residue: 0.5199 time to fit residues: 184.7542 Evaluate side-chains 295 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 8 residue 10 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 166 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 228 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.111377 restraints weight = 35693.497| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.42 r_work: 0.2889 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.313 27007 Z= 0.154 Angle : 0.739 16.446 37074 Z= 0.297 Chirality : 0.040 0.398 3772 Planarity : 0.004 0.067 4374 Dihedral : 18.254 179.992 6147 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.05 % Allowed : 16.98 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.16), residues: 2494 helix: 2.39 (0.12), residues: 1501 sheet: -0.97 (0.78), residues: 41 loop : 0.26 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 44 TYR 0.018 0.002 TYR M 193 PHE 0.023 0.002 PHE L 41 TRP 0.033 0.001 TRP S 6 HIS 0.008 0.002 HIS R 19 Details of bonding type rmsd covalent geometry : bond 0.00356 (26957) covalent geometry : angle 0.73922 (37074) hydrogen bonds : bond 0.04905 ( 1326) hydrogen bonds : angle 4.21931 ( 3748) Misc. bond : bond 0.06460 ( 50) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 266 time to evaluate : 0.681 Fit side-chains REVERT: L 208 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5296 (mppt) REVERT: M 45 ASP cc_start: 0.8282 (t0) cc_final: 0.7838 (m-30) REVERT: H 48 ARG cc_start: 0.7025 (mtp180) cc_final: 0.6720 (mtp85) REVERT: H 253 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6905 (mm-30) REVERT: H 259 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5741 (tp) REVERT: J 24 GLN cc_start: 0.6601 (tt0) cc_final: 0.6213 (tp40) REVERT: J 27 THR cc_start: 0.7385 (m) cc_final: 0.7059 (t) REVERT: P 23 VAL cc_start: 0.7203 (OUTLIER) cc_final: 0.6747 (t) REVERT: P 24 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.6321 (mp-120) REVERT: P 27 THR cc_start: 0.8055 (m) cc_final: 0.7717 (m) REVERT: Q 15 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7270 (mtp180) REVERT: S 15 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.5739 (ttp-170) REVERT: S 17 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7443 (mp) REVERT: Y 38 SER cc_start: 0.8762 (m) cc_final: 0.8515 (p) REVERT: 1 7 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.5681 (mmtp) REVERT: 1 18 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6601 (mp) REVERT: 2 7 MET cc_start: 0.3383 (mmp) cc_final: 0.2555 (tpt) REVERT: 2 25 SER cc_start: 0.7160 (OUTLIER) cc_final: 0.6682 (p) REVERT: 2 27 THR cc_start: 0.7664 (t) cc_final: 0.7308 (m) REVERT: 3 16 MET cc_start: 0.5776 (mmt) cc_final: 0.5411 (tpt) REVERT: 4 7 MET cc_start: 0.4594 (mtm) cc_final: 0.4239 (ptm) REVERT: 6 30 PHE cc_start: 0.8013 (m-10) cc_final: 0.7781 (m-10) REVERT: 7 13 ASP cc_start: 0.7751 (t0) cc_final: 0.7528 (t0) REVERT: 8 26 MET cc_start: 0.8366 (ttm) cc_final: 0.8095 (ttm) outliers start: 44 outliers final: 29 residues processed: 299 average time/residue: 0.5051 time to fit residues: 183.2562 Evaluate side-chains 295 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 157 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 232 optimal weight: 8.9990 chunk 238 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112173 restraints weight = 26669.520| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.03 r_work: 0.2886 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.335 27007 Z= 0.195 Angle : 0.807 16.370 37074 Z= 0.326 Chirality : 0.043 0.403 3772 Planarity : 0.005 0.068 4374 Dihedral : 18.636 179.972 6147 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 17.07 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.16), residues: 2494 helix: 2.23 (0.12), residues: 1500 sheet: -1.02 (0.76), residues: 41 loop : 0.19 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 192 TYR 0.023 0.002 TYR C 319 PHE 0.028 0.002 PHE L 41 TRP 0.041 0.002 TRP S 6 HIS 0.010 0.002 HIS R 19 Details of bonding type rmsd covalent geometry : bond 0.00454 (26957) covalent geometry : angle 0.80660 (37074) hydrogen bonds : bond 0.05290 ( 1326) hydrogen bonds : angle 4.32861 ( 3748) Misc. bond : bond 0.07223 ( 50) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 0.875 Fit side-chains REVERT: L 208 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5328 (mppt) REVERT: M 45 ASP cc_start: 0.8291 (t0) cc_final: 0.7858 (m-30) REVERT: H 253 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6977 (mm-30) REVERT: H 259 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5750 (tp) REVERT: D 41 GLU cc_start: 0.8266 (tp30) cc_final: 0.7836 (tp30) REVERT: F 41 GLU cc_start: 0.8021 (tp30) cc_final: 0.7807 (tp30) REVERT: J 24 GLN cc_start: 0.6592 (tt0) cc_final: 0.6208 (tp40) REVERT: J 27 THR cc_start: 0.7418 (m) cc_final: 0.7099 (t) REVERT: P 24 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6325 (mp-120) REVERT: P 27 THR cc_start: 0.8063 (m) cc_final: 0.7717 (m) REVERT: Q 15 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7307 (mtp180) REVERT: S 15 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.5759 (ttp-170) REVERT: S 17 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7470 (mp) REVERT: 1 7 LYS cc_start: 0.6002 (OUTLIER) cc_final: 0.5731 (mmtp) REVERT: 1 18 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6605 (mp) REVERT: 2 7 MET cc_start: 0.3466 (mmp) cc_final: 0.2641 (tpt) REVERT: 2 25 SER cc_start: 0.7254 (OUTLIER) cc_final: 0.6856 (p) REVERT: 6 30 PHE cc_start: 0.8019 (m-10) cc_final: 0.7784 (m-10) REVERT: 7 13 ASP cc_start: 0.7794 (t0) cc_final: 0.7571 (t0) REVERT: 8 26 MET cc_start: 0.8378 (ttm) cc_final: 0.8127 (ttm) outliers start: 42 outliers final: 29 residues processed: 285 average time/residue: 0.5039 time to fit residues: 170.5870 Evaluate side-chains 286 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 4 optimal weight: 0.0070 chunk 110 optimal weight: 10.0000 chunk 173 optimal weight: 0.0170 chunk 41 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 chunk 175 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 overall best weight: 1.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.150680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113887 restraints weight = 33934.926| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.36 r_work: 0.2901 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.296 27007 Z= 0.140 Angle : 0.717 15.868 37074 Z= 0.289 Chirality : 0.039 0.397 3772 Planarity : 0.004 0.068 4374 Dihedral : 17.885 179.979 6147 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.68 % Allowed : 17.54 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.16), residues: 2494 helix: 2.45 (0.12), residues: 1501 sheet: -0.94 (0.79), residues: 41 loop : 0.27 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 44 TYR 0.018 0.002 TYR M 193 PHE 0.022 0.002 PHE L 41 TRP 0.038 0.001 TRP S 6 HIS 0.008 0.001 HIS R 19 Details of bonding type rmsd covalent geometry : bond 0.00322 (26957) covalent geometry : angle 0.71730 (37074) hydrogen bonds : bond 0.04752 ( 1326) hydrogen bonds : angle 4.18474 ( 3748) Misc. bond : bond 0.06324 ( 50) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11262.14 seconds wall clock time: 191 minutes 51.52 seconds (11511.52 seconds total)